Module 01

Reserve the first level headings (#) for the start of a new Module. This will help to organize your portfolio in an intuitive fashion.
Note: Please edit this template to your heart’s content. This is meant to be the armature upon which you build your individual portfolio. You do not need to keep this instructive text in your final portfolio, although you do need to keep module and assignment names so we can identify what is what.

Module 01 portfolio check

The first of your second level headers (##) is to be used for the portfolio content checks. The Module 01 portfolio check has been built for you directly into this template, but will also be available as a stand-alone markdown document available on the MICB425 GitHub so that you know what is required in each module section in your portfolio. The completion status and comments will be filled in by the instructors during portfolio checks when your current portfolios are pulled from GitHub.

  • Installation check
    • Completion status:
    • Comments:
  • Portfolio repo setup
    • Completion status:
    • Comments:
  • RMarkdown Pretty html Challenge
    • Completion status:
    • Comments:
  • Evidence worksheet_01
    • Completion status:
    • Comments:
  • Evidence worksheet_02
    • Completion status:
    • Comments:
  • Evidence worksheet_03
    • Completion status:
    • Comments:
  • Problem Set_01
    • Completion status:
    • Comments:
  • Problem Set_02
    • Completion status:
    • Comments:
  • Writing assessment_01
    • Completion status:
    • Comments:
  • Additional Readings
    • Completion status:
    • Comments

Data science Friday

The remaining second level headers (##) are for separating data science Friday, regular course, and project content. In this module, you will only need to include data science Friday and regular course content; projects will come later in the course.

Installation check

Third level headers (###) should be used for links to assignments, evidence worksheets, problem sets, and readings, as seen here.

Use this space to include your installation screenshots.

Portfolio repo setup

Detail the code you used to create, initialize, and push your portfolio repo to GitHub. This will be helpful as you will need to repeat many of these steps to update your porfolio throughout the course.

In Git: mkdir MICB425_portfolio cd MICB425_portfolio cd MICB425_portfolio Create repository on GitHub page. git init git add . git commit -m “First commit” git remote add origin https://remote_repository_URL git remote -v git push -u origin master

RMarkdown pretty html challenge

Paste your code from the in-class activity of recreating the example html.

R Markdown PDF Challenge

The following assignment is an exercise for the reproduction of this .html document using the RStudio and RMarkdown tools we’ve shown you in class. Hopefully by the end of this, you won’t feel at all the way this poor PhD student does. We’re here to help, and when it comes to R, the internet is a really valuable resource. This open-source program has all kinds of tutorials online.

http://phdcomics.com/ Comic posted 1-17-2018

http://phdcomics.com/ Comic posted 1-17-2018

Challenge Goals

The goal of this R Markdown html challenge is to give you an opportunity to play with a bunch of different RMarkdown formatting. Consider it a chance to flex your RMarkdown muscles. Your goal is to write your own RMarkdown that rebuilds this html document as close to the original as possible. So, yes, this means you get to copy my irreverant tone exactly in your own Markdowns. It’s a little window into my psyche. Enjoy =)
hint: go to the PhD Comics website to see if you can find the image above
If you can’t find the exact image, just find a comparable from the PhD Comics website and include it in your markdown

Here’s a header!

Let’s be honest, this header is a little arbitrary. But show me that you can reproduce headers with different levels please. This is a level 3 header, for your reference (you can most easily tell this from the table of contents).

Another header, now with maths

Perhaps you’re already really confused by the whole markdown thing. Maybe you’re so confused that you’ve forgotton how to add. Never fear!A calculator R is here:

1231521+12341556280987
## [1] 1.234156e+13

Table Time

Or maybe, after you’ve added those numbers, you feel like it’s about time for a table! I’m going to leave all the guts of the coding here so you can see how libraries (R packages) are loaded into R (more on that later). It’s not terribly pretty, but it hints at how R works and how you will use it in the future. The summary function used below is a nice data exploration function that you may use in thefuture.

library(knitr)
kable(summary(cars),caption="I made this table with kable in the knitr package library")
I made this table with kable in the knitr package library
speed dist
Min. : 4.0 Min. : 2.00
1st Qu.:12.0 1st Qu.: 26.00
Median :15.0 Median : 36.00
Mean :15.4 Mean : 42.98
3rd Qu.:19.0 3rd Qu.: 56.00
Max. :25.0 Max. :120.00

And now you’ve almost finished your first RMarkdown! Feeling excited? We are! In fact, we’re so excited that maybe we need a big finale eh?
Here’s ours! Include a fun gif of your choice!

Silicon Valley

Silicon Valley

Origins and Earth Systems

Evidence worksheet 01

The template for the first Evidence Worksheet has been included here. The first thing for any assignment should link(s) to any relevant literature (which should be included as full citations in a module references section below).

You can copy-paste in the answers you recorded when working through the evidence worksheet into this portfolio template.

As you include Evidence worksheets and Problem sets in the future, ensure that you delineate Questions/Learning Objectives/etc. by using headers that are 4th level and greater. This will still create header markings when you render (knit) the document, but will exclude these levels from the Table of Contents. That’s a good thing. You don’t’ want to clutter the Table of Contents too much.

Whitman et al 1998

Learning objectives

Describe the numerical abundance of microbial life in relation to ecology and biogeochemistry of Earth systems.

General questions

  • What were the main questions being asked?
    What is the abundance of prokaryotes on earth? What is the total amount of cellular carbon produced by these prokaryotes on earth?

  • What were the primary methodological approaches used?
    To count prokaryotes
    • aquatic environments: used cellular density
    • soil: direct counts from a coniferous forest ultisol (cells/g)
      • unpublished field studies of E. A. Paul for cultivated soils
      • terrestrial subsurface
      • unconsolidated sediments represent most of marine subsurface and have been determined
      • assuming that average porosity of terrestrial subsurface is 3%
      • estimation from groundwater data based on values from seven sites and four studies

Other Habitats: - animals - human: cell density of prokaryotes on the skin multiply by skin surface area - insects like termite by counting number of insect and number of prokaryotes in said insect - leaves: can be estimated by assuming a dense population and high leaf area index
- air: pre-calculated Carbon Content: - estimated from cell numbers in soil, aquatic systems, and the subsurface - cellular carbon is assumed to be one-half of dry weight for soil and subsurface - take average dry weight of prokaryotic cells multiple by number of cell - aquatic systems: assumed that average cellular carbon for sedimentary and planktonic prokaryotes to be 10 and 20 fg of C/cell respectively then multiple that with number of cells in aquatic systems

  • Summarize the main results or findings.
    • Total number of prokaryotes is 4-6 x 1030 cells and 350-500 Pg of C (1 Pg = 1015 g)
    • Represent the largest pool of nutrients such as N and P Essentially, prokaryotic biomass as a major contributor to total biosphere
  • Do new questions arise from the results?
    • what is the genetic diversity of these prokaryotes?
    • The number of prokaryotic species? How does prokaryotic turnover affect carbon fixation and carbon cycle?
  • Were there any specific challenges or advantages in understanding the paper (e.g. did the authors provide sufficient background information to understand experimental logic, were methods explained adequately, were any specific assumptions made, were conclusions justified based on the evidence, were the figures or tables useful and easy to understand)?
    • bombards you with numbers
    • inadequate explanation of some assumptions made especially when estimating carbon content
    • can be found in literature however
    • assumed that the papers they cited had the proper methods
    • lots of estimation of cell densities

Evidence Worksheet_02 “Life and the Evolution of Earth’s Atmosphere”

Learning objectives:

Comment on the emergence of microbial life and the evolution of Earth systems

  • Indicate the key events in the evolution of Earth systems at each approximate moment in the time series. If times need to be adjusted or added to the timeline to fully account for the development of Earth systems, please do so.

    • 4.6 billion years ago

    • Formation of Earth

    • 4.5 billion years ago

    • Moon was formed to give Earth spin & tilt, day & night cycles, seasons

    • 4.4 billion years ago

    • oldest mineral found (zircon)

    • 4.1 billion years ago

    • earliest evidence of life in zircon

    • 3.8 billion years ago
    • meteor bombardment stops
    • Sedimentary rocks: weathering, ocean
    • carbon isotopes also in graphite

    • iron rich sedimentary rocks

    • 3.5 billion years ago
    • Photosynthesis: ambigious microfossils

    • stromatolites (organosedimentary structures produced by microbial trappings, usually but not always photosynthetic)

    • 3.0 billion years ago

    • Glaciation: Earth would have appeared brown

    • 2.2 billion years ago
    • oxygen levels increased sharply

    • rock recognized as redbeds -> evidence for oxidation

    • 2.1 billion years ago

    • end of Snowball Earth

    • 1.9 billion years ago

    • Eukaryote emergence

    • 1.3 billion years ago

    • 550 million years ago

    • Cambrian explosion

    • 400 million years ago

    • emergence of land plants

    • 200,000 years ago

    • H. Sapiens appear

  • Describe the dominant physical and chemical characteristics of Earth systems at the following waypoints:

    • Hadean
    • extremely hot >100oC ocean temperature

    • seawater chemistry controlled by volcanism

    • Archean

    • methanogenesis (early); Greenhouse effect because of CH4 and CO2

    • Precambrian
    • reducing atmosphere
    • glaciation ended as greenhouse effec was enhanced by volcanoes

    • CO2 levels hundrends times higher than now

    • Proterozoic
    • Snowball Earth
    • accumulation of oxygen in the Earth’s atmosphere
    • filling of chemical sinks and increase carbon burtial

    • nitrogen concentration close to modern levels

    • Phanerozoic
    • carboniferous period
    • four separate glaciation periods

    • higher oxygen levels

Problem set 01

Learning objectives:

Describe the numerical abundance of microbial life in relation to the ecology and biogeochemistry of Earth systems.

Specific questions:

  • What are the primary prokaryotic habitats on Earth and how do they vary with respect to their capacity to support life? Provide a breakdown of total cell abundance for each primary habitat from the tables provided in the text.

    a. Aquatic : 1.18 x 10^29^
b. Soil: 2.556 x 10^29^
    1. subsurface: 3.8 x 1030

  • What is the estimated prokaryotic cell abundance in the upper 200 m of the ocean and what fraction of this biomass is represented by marine cyanobacterium including Prochlorococcus? What is the significance of this ratio with respect to carbon cycling in the ocean and the atmospheric composition of the Earth? 3.6 x 1028 cyanobacteria: 4x 104 cells/ml / 5 x 105 cells x 100 = 8%

  • What is the difference between an autotroph, heterotroph, and a lithotroph based on information provided in the text?
    a. autotroph: “self-nourishing” fix inorganic carbon (CO2) -> biomass b. heterotroph: assimilate organic carbon
    1. lithotroph: use inorganic substances

  • Based on information provided in the text and your knowledge of geography what is the deepest habitat capable of supporting prokaryotic life? What is the primary limiting factor at this depth?

Since the temperature drop is 22 degrees drop per km so the deepest part that can support life is Mariana Trench 10.9km + plus an extra 5 km

  • Based on information provided in the text your knowledge of geography what is the highest habitat capable of supporting prokaryotic life? What is the primary limiting factor at this height?
    22 km on top of the 8.8 km on Mt. Everest. A limiting factor at that height would be obtaining enough nutrients.

  • Based on estimates of prokaryotic habitat limitation, what is the vertical distance of the Earth’s biosphere measured in km?

22 + 8.8 + 10.9 + 5 = 46.7 km

  • How was annual cellular production of prokaryotes described in Table 7 column four determined? (Provide an example of the calculation)
    - 3.6 x 1028 / 16 x 365 = 8.4 x 1029 - population size divided by turnover time per day times 365 days

  • What is the relationship between carbon content, carbon assimilation efficiency and turnover rates in the upper 200m of the ocean? Why does this vary with depth in the ocean and between terrestrial and marine habitats?
    • carbon efficiency is 20%
    • 5-20 fg C/cell
    • (3.6 x 1026 Pg/cell)(20x1030 cell) = 0.72 Pg of C in marine heterotrophs
  • How were the frequency numbers for four simultaneous mutations in shared genes determined for marine heterotrophs and marine autotrophs given an average mutation rate of 4 x 10-7 per DNA replication? (Provide an example of the calculation with units. Hint: cell and generation cancel out)
    • 4 x 10-7 mutations/generation -(4 x 10-7-)4 = 2.56 x 10-26 mutations/generation
    • 365/16 = 22.5 turnovers/yr -(3.1 x 1028 cells) x 22.5 = 8.2 x 1029 cells/yr -(8.2 x 1029 cells/yr)(2.56 x 10-26 mutations/generation) = 2.1 x 104 mutations/yr

  • Given the large population size and high mutation rate of prokaryotic cells, what are the implications with respect to genetic diversity and adaptive potential? Are point mutations the only way in which microbial genomes diversify and adapt?

  • Prokaryotes would have high genetic diversity and the ability to adapt quickly dude to their high mutation rate. Insertions and deletions are generally detrimental to a gene’s function since they shift the reading frame so point mutations tend to be the most common, but there’s potential for these type of mutations to promote genetic diversity.

  • What relationships can be inferred between prokaryotic abundance, diversity, and metabolic potential based on the information provided in the text?

  • High prokaryotic abundance encourages the diversification of metabolic capabilities in prokaryotes. There are more likely to be more mutations taking place in a larger population of prokaryotes that allow them to fully take advantage of their environment and compete for different resources.

Problem set_02 “Microbial Engines”

Learning objectives:

Discuss the role of microbial diversity and formation of coupled metabolism in driving global biogeochemical cycles.

Specific Questions:

  • What are the primary geophysical and biogeochemical processes that create and sustain conditions for life on Earth? How do abiotic versus biotic processes vary with respect to matter and energy transformation and how are they interconnected?
  • The primary geophysical processs is tectonics and the atmospheric protochemical process is the biochemical process that create geochemical cycles.
  • abiotic processes are based on acid/base chemistry
  • biotic processes are dependent on redox reactions

  • abiotic processes are a source of nutrients for biotic reactions

  • Why is Earth’s redox state considered an emergent property?
  • biogechemical cycles of microbial life evolved to form nested abiotically driven acid-base redox reactions
  • these reactions over time altered the redox state of the planet

  • result of a collective complex system made up of individual microbes

  • How do reversible electron transfer reactions give rise to element and nutrient cycles at different ecological scales? What strategies do microbes use to overcome thermodynamic barriers to reversible electron flow?
  • the reduction or oxidation of elements allows them to assimilate or dissmilate nutrients, leading to the recycling of nutrient cycles

  • overcome thermodynamic barriers with synergistic cooperation of multispeicies assemblages

  • Using information provided in the text, describe how the nitrogen cycle partitions between different redox “niches” and microbial groups. Is there a relationship between the nitrogen cycle and climate change?
  • NH4+ is oxidized in a two-step manner, first requiring a group of Bacteria or Archaea to oxidize ammonia to NO2-, then oxidized to NO3+-+ by different suite of nitrifying bacteria
  • third set of microbes uses NO2+-+ and NO3+-+ as electron acceptors to form N2
  • incomplete reduction of nirate or nitrite due to excess nitrogen being introduced to the nitrogen cycle leads to accumulation of nitrous oxide

  • nitrous oxide is a potent greenhosue gass that contributes to global warming

  • What is the relationship between microbial diversity and metabolic diversity and how does this relate to the discovery of new protein families from microbial community genomes?
  • linear relationship between number of nonreduandant (diverse) microbiaal seuqneces and the discovery of new protein families
  • but metabolic machinery is highly conserved between microbes, so microbial diversity does not lead to metabolic diversity
  • On what basis do the authors consider microbes the guardians of metabolism?

  • microbes have core planetary gene set dispersed to them through vertical or horizontal gene transfer allow them to protect the metabolic pathway

Module 01 references

Utilize this space to include a bibliography of any literature you want associated with this module. We recommend keeping this as the final header under each module.

An example for Whitman and Wiebe (1998) has been included below.

Whitman WB, Coleman DC, and Wiebe WJ. 1998. Prokaryotes: The unseen majority. Proc Natl Acad Sci USA. 95(12):6578–6583. PMC33863

Kasting JF, Siefert JL. 2002. Life and the evolution of earth â€TM s atmosphere. Library (Lond) 296:1066–1069.

Canfield DE, Glazer AN, Falkowski PG. 2010. The evolution and future of earth’s nitrogen cycle. Science (80- ) 330:192–196.

Falkowski PG, Fenchel T, Delong EF. 2008. The microbial engines that drive earth’s biogeochemical cycles. Science (80- ) 320:1034–1039.